sequenzo 0.1.18__cp312-cp312-macosx_10_13_universal2.whl → 0.1.19__cp312-cp312-macosx_10_13_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h

@@ -1,254 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2011-2014 Gael Guennebaud <gael.guennebaud@inria.fr>
-// Copyright (C) 2010 Daniel Lowengrub <lowdanie@gmail.com>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_SPARSEVIEW_H
-#define EIGEN_SPARSEVIEW_H
-
-namespace Eigen { 
-
-namespace internal {
-
-template<typename MatrixType>
-struct traits<SparseView<MatrixType> > : traits<MatrixType>
-{
-  typedef typename MatrixType::StorageIndex StorageIndex;
-  typedef Sparse StorageKind;
-  enum {
-    Flags = int(traits<MatrixType>::Flags) & (RowMajorBit)
-  };
-};
-
-} // end namespace internal
-
-/** \ingroup SparseCore_Module
-  * \class SparseView
-  *
-  * \brief Expression of a dense or sparse matrix with zero or too small values removed
-  *
-  * \tparam MatrixType the type of the object of which we are removing the small entries
-  *
-  * This class represents an expression of a given dense or sparse matrix with
-  * entries smaller than \c reference * \c epsilon are removed.
-  * It is the return type of MatrixBase::sparseView() and SparseMatrixBase::pruned()
-  * and most of the time this is the only way it is used.
-  *
-  * \sa MatrixBase::sparseView(), SparseMatrixBase::pruned()
-  */
-template<typename MatrixType>
-class SparseView : public SparseMatrixBase<SparseView<MatrixType> >
-{
-  typedef typename MatrixType::Nested MatrixTypeNested;
-  typedef typename internal::remove_all<MatrixTypeNested>::type _MatrixTypeNested;
-  typedef SparseMatrixBase<SparseView > Base;
-public:
-  EIGEN_SPARSE_PUBLIC_INTERFACE(SparseView)
-  typedef typename internal::remove_all<MatrixType>::type NestedExpression;
-
-  explicit SparseView(const MatrixType& mat, const Scalar& reference = Scalar(0),
-                      const RealScalar &epsilon = NumTraits<Scalar>::dummy_precision())
-    : m_matrix(mat), m_reference(reference), m_epsilon(epsilon) {}
-
-  inline Index rows() const { return m_matrix.rows(); }
-  inline Index cols() const { return m_matrix.cols(); }
-
-  inline Index innerSize() const { return m_matrix.innerSize(); }
-  inline Index outerSize() const { return m_matrix.outerSize(); }
-  
-  /** \returns the nested expression */
-  const typename internal::remove_all<MatrixTypeNested>::type&
-  nestedExpression() const { return m_matrix; }
-  
-  Scalar reference() const { return m_reference; }
-  RealScalar epsilon() const { return m_epsilon; }
-  
-protected:
-  MatrixTypeNested m_matrix;
-  Scalar m_reference;
-  RealScalar m_epsilon;
-};
-
-namespace internal {
-
-// TODO find a way to unify the two following variants
-// This is tricky because implementing an inner iterator on top of an IndexBased evaluator is
-// not easy because the evaluators do not expose the sizes of the underlying expression.
-  
-template<typename ArgType>
-struct unary_evaluator<SparseView<ArgType>, IteratorBased>
-  : public evaluator_base<SparseView<ArgType> >
-{
-    typedef typename evaluator<ArgType>::InnerIterator EvalIterator;
-  public:
-    typedef SparseView<ArgType> XprType;
-    
-    class InnerIterator : public EvalIterator
-    {
-      protected:
-        typedef typename XprType::Scalar Scalar;
-      public:
-
-        EIGEN_STRONG_INLINE InnerIterator(const unary_evaluator& sve, Index outer)
-          : EvalIterator(sve.m_argImpl,outer), m_view(sve.m_view)
-        {
-          incrementToNonZero();
-        }
-
-        EIGEN_STRONG_INLINE InnerIterator& operator++()
-        {
-          EvalIterator::operator++();
-          incrementToNonZero();
-          return *this;
-        }
-
-        using EvalIterator::value;
-
-      protected:
-        const XprType &m_view;
-
-      private:
-        void incrementToNonZero()
-        {
-          while((bool(*this)) && internal::isMuchSmallerThan(value(), m_view.reference(), m_view.epsilon()))
-          {
-            EvalIterator::operator++();
-          }
-        }
-    };
-    
-    enum {
-      CoeffReadCost = evaluator<ArgType>::CoeffReadCost,
-      Flags = XprType::Flags
-    };
-    
-    explicit unary_evaluator(const XprType& xpr) : m_argImpl(xpr.nestedExpression()), m_view(xpr) {}
-
-  protected:
-    evaluator<ArgType> m_argImpl;
-    const XprType &m_view;
-};
-
-template<typename ArgType>
-struct unary_evaluator<SparseView<ArgType>, IndexBased>
-  : public evaluator_base<SparseView<ArgType> >
-{
-  public:
-    typedef SparseView<ArgType> XprType;
-  protected:
-    enum { IsRowMajor = (XprType::Flags&RowMajorBit)==RowMajorBit };
-    typedef typename XprType::Scalar Scalar;
-    typedef typename XprType::StorageIndex StorageIndex;
-  public:
-    
-    class InnerIterator
-    {
-      public:
-
-        EIGEN_STRONG_INLINE InnerIterator(const unary_evaluator& sve, Index outer)
-          : m_sve(sve), m_inner(0), m_outer(outer), m_end(sve.m_view.innerSize())
-        {
-          incrementToNonZero();
-        }
-
-        EIGEN_STRONG_INLINE InnerIterator& operator++()
-        {
-          m_inner++;
-          incrementToNonZero();
-          return *this;
-        }
-
-        EIGEN_STRONG_INLINE Scalar value() const
-        {
-          return (IsRowMajor) ? m_sve.m_argImpl.coeff(m_outer, m_inner)
-                              : m_sve.m_argImpl.coeff(m_inner, m_outer);
-        }
-
-        EIGEN_STRONG_INLINE StorageIndex index() const { return m_inner; }
-        inline Index row() const { return IsRowMajor ? m_outer : index(); }
-        inline Index col() const { return IsRowMajor ? index() : m_outer; }
-
-        EIGEN_STRONG_INLINE operator bool() const { return m_inner < m_end && m_inner>=0; }
-
-      protected:
-        const unary_evaluator &m_sve;
-        Index m_inner;
-        const Index m_outer;
-        const Index m_end;
-
-      private:
-        void incrementToNonZero()
-        {
-          while((bool(*this)) && internal::isMuchSmallerThan(value(), m_sve.m_view.reference(), m_sve.m_view.epsilon()))
-          {
-            m_inner++;
-          }
-        }
-    };
-    
-    enum {
-      CoeffReadCost = evaluator<ArgType>::CoeffReadCost,
-      Flags = XprType::Flags
-    };
-    
-    explicit unary_evaluator(const XprType& xpr) : m_argImpl(xpr.nestedExpression()), m_view(xpr) {}
-
-  protected:
-    evaluator<ArgType> m_argImpl;
-    const XprType &m_view;
-};
-
-} // end namespace internal
-
-/** \ingroup SparseCore_Module
-  *
-  * \returns a sparse expression of the dense expression \c *this with values smaller than
-  * \a reference * \a epsilon removed.
-  *
-  * This method is typically used when prototyping to convert a quickly assembled dense Matrix \c D to a SparseMatrix \c S:
-  * \code
-  * MatrixXd D(n,m);
-  * SparseMatrix<double> S;
-  * S = D.sparseView();             // suppress numerical zeros (exact)
-  * S = D.sparseView(reference);
-  * S = D.sparseView(reference,epsilon);
-  * \endcode
-  * where \a reference is a meaningful non zero reference value,
-  * and \a epsilon is a tolerance factor defaulting to NumTraits<Scalar>::dummy_precision().
-  *
-  * \sa SparseMatrixBase::pruned(), class SparseView */
-template<typename Derived>
-const SparseView<Derived> MatrixBase<Derived>::sparseView(const Scalar& reference,
-                                                          const typename NumTraits<Scalar>::Real& epsilon) const
-{
-  return SparseView<Derived>(derived(), reference, epsilon);
-}
-
-/** \returns an expression of \c *this with values smaller than
-  * \a reference * \a epsilon removed.
-  *
-  * This method is typically used in conjunction with the product of two sparse matrices
-  * to automatically prune the smallest values as follows:
-  * \code
-  * C = (A*B).pruned();             // suppress numerical zeros (exact)
-  * C = (A*B).pruned(ref);
-  * C = (A*B).pruned(ref,epsilon);
-  * \endcode
-  * where \c ref is a meaningful non zero reference value.
-  * */
-template<typename Derived>
-const SparseView<Derived>
-SparseMatrixBase<Derived>::pruned(const Scalar& reference,
-                                  const RealScalar& epsilon) const
-{
-  return SparseView<Derived>(derived(), reference, epsilon);
-}
-
-} // end namespace Eigen
-
-#endif

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h

@@ -1,315 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008 Gael Guennebaud <gael.guennebaud@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_SPARSETRIANGULARSOLVER_H
-#define EIGEN_SPARSETRIANGULARSOLVER_H
-
-namespace Eigen { 
-
-namespace internal {
-
-template<typename Lhs, typename Rhs, int Mode,
-  int UpLo = (Mode & Lower)
-           ? Lower
-           : (Mode & Upper)
-           ? Upper
-           : -1,
-  int StorageOrder = int(traits<Lhs>::Flags) & RowMajorBit>
-struct sparse_solve_triangular_selector;
-
-// forward substitution, row-major
-template<typename Lhs, typename Rhs, int Mode>
-struct sparse_solve_triangular_selector<Lhs,Rhs,Mode,Lower,RowMajor>
-{
-  typedef typename Rhs::Scalar Scalar;
-  typedef evaluator<Lhs> LhsEval;
-  typedef typename evaluator<Lhs>::InnerIterator LhsIterator;
-  static void run(const Lhs& lhs, Rhs& other)
-  {
-    LhsEval lhsEval(lhs);
-    for(Index col=0 ; col<other.cols() ; ++col)
-    {
-      for(Index i=0; i<lhs.rows(); ++i)
-      {
-        Scalar tmp = other.coeff(i,col);
-        Scalar lastVal(0);
-        Index lastIndex = 0;
-        for(LhsIterator it(lhsEval, i); it; ++it)
-        {
-          lastVal = it.value();
-          lastIndex = it.index();
-          if(lastIndex==i)
-            break;
-          tmp -= lastVal * other.coeff(lastIndex,col);
-        }
-        if (Mode & UnitDiag)
-          other.coeffRef(i,col) = tmp;
-        else
-        {
-          eigen_assert(lastIndex==i);
-          other.coeffRef(i,col) = tmp/lastVal;
-        }
-      }
-    }
-  }
-};
-
-// backward substitution, row-major
-template<typename Lhs, typename Rhs, int Mode>
-struct sparse_solve_triangular_selector<Lhs,Rhs,Mode,Upper,RowMajor>
-{
-  typedef typename Rhs::Scalar Scalar;
-  typedef evaluator<Lhs> LhsEval;
-  typedef typename evaluator<Lhs>::InnerIterator LhsIterator;
-  static void run(const Lhs& lhs, Rhs& other)
-  {
-    LhsEval lhsEval(lhs);
-    for(Index col=0 ; col<other.cols() ; ++col)
-    {
-      for(Index i=lhs.rows()-1 ; i>=0 ; --i)
-      {
-        Scalar tmp = other.coeff(i,col);
-        Scalar l_ii(0);
-        LhsIterator it(lhsEval, i);
-        while(it && it.index()<i)
-          ++it;
-        if(!(Mode & UnitDiag))
-        {
-          eigen_assert(it && it.index()==i);
-          l_ii = it.value();
-          ++it;
-        }
-        else if (it && it.index() == i)
-          ++it;
-        for(; it; ++it)
-        {
-          tmp -= it.value() * other.coeff(it.index(),col);
-        }
-
-        if (Mode & UnitDiag)  other.coeffRef(i,col) = tmp;
-        else                  other.coeffRef(i,col) = tmp/l_ii;
-      }
-    }
-  }
-};
-
-// forward substitution, col-major
-template<typename Lhs, typename Rhs, int Mode>
-struct sparse_solve_triangular_selector<Lhs,Rhs,Mode,Lower,ColMajor>
-{
-  typedef typename Rhs::Scalar Scalar;
-  typedef evaluator<Lhs> LhsEval;
-  typedef typename evaluator<Lhs>::InnerIterator LhsIterator;
-  static void run(const Lhs& lhs, Rhs& other)
-  {
-    LhsEval lhsEval(lhs);
-    for(Index col=0 ; col<other.cols() ; ++col)
-    {
-      for(Index i=0; i<lhs.cols(); ++i)
-      {
-        Scalar& tmp = other.coeffRef(i,col);
-        if (tmp!=Scalar(0)) // optimization when other is actually sparse
-        {
-          LhsIterator it(lhsEval, i);
-          while(it && it.index()<i)
-            ++it;
-          if(!(Mode & UnitDiag))
-          {
-            eigen_assert(it && it.index()==i);
-            tmp /= it.value();
-          }
-          if (it && it.index()==i)
-            ++it;
-          for(; it; ++it)
-            other.coeffRef(it.index(), col) -= tmp * it.value();
-        }
-      }
-    }
-  }
-};
-
-// backward substitution, col-major
-template<typename Lhs, typename Rhs, int Mode>
-struct sparse_solve_triangular_selector<Lhs,Rhs,Mode,Upper,ColMajor>
-{
-  typedef typename Rhs::Scalar Scalar;
-  typedef evaluator<Lhs> LhsEval;
-  typedef typename evaluator<Lhs>::InnerIterator LhsIterator;
-  static void run(const Lhs& lhs, Rhs& other)
-  {
-    LhsEval lhsEval(lhs);
-    for(Index col=0 ; col<other.cols() ; ++col)
-    {
-      for(Index i=lhs.cols()-1; i>=0; --i)
-      {
-        Scalar& tmp = other.coeffRef(i,col);
-        if (tmp!=Scalar(0)) // optimization when other is actually sparse
-        {
-          if(!(Mode & UnitDiag))
-          {
-            // TODO replace this by a binary search. make sure the binary search is safe for partially sorted elements
-            LhsIterator it(lhsEval, i);
-            while(it && it.index()!=i)
-              ++it;
-            eigen_assert(it && it.index()==i);
-            other.coeffRef(i,col) /= it.value();
-          }
-          LhsIterator it(lhsEval, i);
-          for(; it && it.index()<i; ++it)
-            other.coeffRef(it.index(), col) -= tmp * it.value();
-        }
-      }
-    }
-  }
-};
-
-} // end namespace internal
-
-#ifndef EIGEN_PARSED_BY_DOXYGEN
-
-template<typename ExpressionType,unsigned int Mode>
-template<typename OtherDerived>
-void TriangularViewImpl<ExpressionType,Mode,Sparse>::solveInPlace(MatrixBase<OtherDerived>& other) const
-{
-  eigen_assert(derived().cols() == derived().rows() && derived().cols() == other.rows());
-  eigen_assert((!(Mode & ZeroDiag)) && bool(Mode & (Upper|Lower)));
-
-  enum { copy = internal::traits<OtherDerived>::Flags & RowMajorBit };
-
-  typedef typename internal::conditional<copy,
-    typename internal::plain_matrix_type_column_major<OtherDerived>::type, OtherDerived&>::type OtherCopy;
-  OtherCopy otherCopy(other.derived());
-
-  internal::sparse_solve_triangular_selector<ExpressionType, typename internal::remove_reference<OtherCopy>::type, Mode>::run(derived().nestedExpression(), otherCopy);
-
-  if (copy)
-    other = otherCopy;
-}
-#endif
-
-// pure sparse path
-
-namespace internal {
-
-template<typename Lhs, typename Rhs, int Mode,
-  int UpLo = (Mode & Lower)
-           ? Lower
-           : (Mode & Upper)
-           ? Upper
-           : -1,
-  int StorageOrder = int(Lhs::Flags) & (RowMajorBit)>
-struct sparse_solve_triangular_sparse_selector;
-
-// forward substitution, col-major
-template<typename Lhs, typename Rhs, int Mode, int UpLo>
-struct sparse_solve_triangular_sparse_selector<Lhs,Rhs,Mode,UpLo,ColMajor>
-{
-  typedef typename Rhs::Scalar Scalar;
-  typedef typename promote_index_type<typename traits<Lhs>::StorageIndex,
-                                      typename traits<Rhs>::StorageIndex>::type StorageIndex;
-  static void run(const Lhs& lhs, Rhs& other)
-  {
-    const bool IsLower = (UpLo==Lower);
-    AmbiVector<Scalar,StorageIndex> tempVector(other.rows()*2);
-    tempVector.setBounds(0,other.rows());
-
-    Rhs res(other.rows(), other.cols());
-    res.reserve(other.nonZeros());
-
-    for(Index col=0 ; col<other.cols() ; ++col)
-    {
-      // FIXME estimate number of non zeros
-      tempVector.init(.99/*float(other.col(col).nonZeros())/float(other.rows())*/);
-      tempVector.setZero();
-      tempVector.restart();
-      for (typename Rhs::InnerIterator rhsIt(other, col); rhsIt; ++rhsIt)
-      {
-        tempVector.coeffRef(rhsIt.index()) = rhsIt.value();
-      }
-
-      for(Index i=IsLower?0:lhs.cols()-1;
-          IsLower?i<lhs.cols():i>=0;
-          i+=IsLower?1:-1)
-      {
-        tempVector.restart();
-        Scalar& ci = tempVector.coeffRef(i);
-        if (ci!=Scalar(0))
-        {
-          // find
-          typename Lhs::InnerIterator it(lhs, i);
-          if(!(Mode & UnitDiag))
-          {
-            if (IsLower)
-            {
-              eigen_assert(it.index()==i);
-              ci /= it.value();
-            }
-            else
-              ci /= lhs.coeff(i,i);
-          }
-          tempVector.restart();
-          if (IsLower)
-          {
-            if (it.index()==i)
-              ++it;
-            for(; it; ++it)
-              tempVector.coeffRef(it.index()) -= ci * it.value();
-          }
-          else
-          {
-            for(; it && it.index()<i; ++it)
-              tempVector.coeffRef(it.index()) -= ci * it.value();
-          }
-        }
-      }
-
-
-      Index count = 0;
-      // FIXME compute a reference value to filter zeros
-      for (typename AmbiVector<Scalar,StorageIndex>::Iterator it(tempVector/*,1e-12*/); it; ++it)
-      {
-        ++ count;
-//         std::cerr << "fill " << it.index() << ", " << col << "\n";
-//         std::cout << it.value() << "  ";
-        // FIXME use insertBack
-        res.insert(it.index(), col) = it.value();
-      }
-//       std::cout << "tempVector.nonZeros() == " << int(count) << " / " << (other.rows()) << "\n";
-    }
-    res.finalize();
-    other = res.markAsRValue();
-  }
-};
-
-} // end namespace internal
-
-#ifndef EIGEN_PARSED_BY_DOXYGEN
-template<typename ExpressionType,unsigned int Mode>
-template<typename OtherDerived>
-void TriangularViewImpl<ExpressionType,Mode,Sparse>::solveInPlace(SparseMatrixBase<OtherDerived>& other) const
-{
-  eigen_assert(derived().cols() == derived().rows() && derived().cols() == other.rows());
-  eigen_assert( (!(Mode & ZeroDiag)) && bool(Mode & (Upper|Lower)));
-
-//   enum { copy = internal::traits<OtherDerived>::Flags & RowMajorBit };
-
-//   typedef typename internal::conditional<copy,
-//     typename internal::plain_matrix_type_column_major<OtherDerived>::type, OtherDerived&>::type OtherCopy;
-//   OtherCopy otherCopy(other.derived());
-
-  internal::sparse_solve_triangular_sparse_selector<ExpressionType, OtherDerived, Mode>::run(derived().nestedExpression(), other.derived());
-
-//   if (copy)
-//     other = otherCopy;
-}
-#endif
-
-} // end namespace Eigen
-
-#endif // EIGEN_SPARSETRIANGULARSOLVER_H